Analysis date: 2023-08-08
CRC_Xenografts_Batch2_DataProcessing Script
load("../Data/Cache/Xenografts_Batch2_DataProcessing.RData")sample_annotation_df <- tibble( sample = rownames(
pY_mat_Set5_normXenograft1_normtomedian
) ) %>%
separate(col = sample, sep = "_",
into = c("log2FC", "xenograft", "treatment",
"timepoint", "replicate", "set" ), remove = F) %>%
column_to_rownames("sample") %>% select(-log2FC)
t(pY_mat_Set5_normXenograft1_normtomedian) %>%
plot_centered_heatmaply_around_nochange(
labCol = sub("log2FC_", "", rownames(pY_mat_Set5_normXenograft1_normtomedian)),
col_side_colors = sample_annotation_df)sample_annotation_df <- tibble( sample = rownames(
pST_mat_Set5_normXenograft1_normtomedian
) ) %>%
separate(col = sample, sep = "_",
into = c("log2FC", "xenograft", "treatment",
"timepoint", "replicate", "set" ), remove = F) %>%
column_to_rownames("sample") %>% select(-log2FC)
t(pST_mat_Set5_normXenograft1_normtomedian) %>%
plot_centered_heatmaply_around_nochange(
labCol = sub("log2FC_", "", rownames(
pST_mat_Set5_normXenograft1_normtomedian
)),
col_side_colors = sample_annotation_df)sessionInfo()## R version 4.2.3 (2023-03-15)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur ... 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] lubridate_1.9.2 forcats_1.0.0
## [3] stringr_1.5.0 dplyr_1.1.2
## [5] purrr_1.0.1 readr_2.1.4
## [7] tidyr_1.3.0 tibble_3.2.1
## [9] ggplot2_3.4.2 tidyverse_2.0.0
## [11] mdatools_0.14.0 SummarizedExperiment_1.28.0
## [13] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
## [15] MatrixGenerics_1.10.0 matrixStats_1.0.0
## [17] DEP_1.20.0 org.Hs.eg.db_3.16.0
## [19] AnnotationDbi_1.60.2 IRanges_2.32.0
## [21] S4Vectors_0.36.2 Biobase_2.58.0
## [23] BiocGenerics_0.44.0 fgsea_1.24.0
##
## loaded via a namespace (and not attached):
## [1] circlize_0.4.15 fastmatch_1.1-3 plyr_1.8.8
## [4] igraph_1.5.0.1 gmm_1.8 lazyeval_0.2.2
## [7] shinydashboard_0.7.2 crosstalk_1.2.0 BiocParallel_1.32.6
## [10] digest_0.6.33 ca_0.71.1 foreach_1.5.2
## [13] htmltools_0.5.5 viridis_0.6.4 fansi_1.0.4
## [16] magrittr_2.0.3 memoise_2.0.1 cluster_2.1.4
## [19] doParallel_1.0.17 tzdb_0.4.0 limma_3.54.2
## [22] ComplexHeatmap_2.14.0 Biostrings_2.66.0 imputeLCMD_2.1
## [25] sandwich_3.0-2 timechange_0.2.0 colorspace_2.1-0
## [28] blob_1.2.4 xfun_0.39 crayon_1.5.2
## [31] RCurl_1.98-1.12 jsonlite_1.8.7 impute_1.72.3
## [34] zoo_1.8-12 iterators_1.0.14 glue_1.6.2
## [37] hash_2.2.6.2 registry_0.5-1 gtable_0.3.3
## [40] zlibbioc_1.44.0 XVector_0.38.0 webshot_0.5.5
## [43] GetoptLong_1.0.5 DelayedArray_0.24.0 shape_1.4.6
## [46] scales_1.2.1 vsn_3.66.0 mvtnorm_1.2-2
## [49] DBI_1.1.3 Rcpp_1.0.11 plotrix_3.8-2
## [52] mzR_2.32.0 viridisLite_0.4.2 xtable_1.8-4
## [55] clue_0.3-64 bit_4.0.5 preprocessCore_1.60.2
## [58] sqldf_0.4-11 MsCoreUtils_1.10.0 DT_0.28
## [61] htmlwidgets_1.6.2 httr_1.4.6 gplots_3.1.3
## [64] RColorBrewer_1.1-3 ellipsis_0.3.2 farver_2.1.1
## [67] pkgconfig_2.0.3 XML_3.99-0.14 sass_0.4.7
## [70] utf8_1.2.3 STRINGdb_2.10.1 labeling_0.4.2
## [73] reshape2_1.4.4 tidyselect_1.2.0 rlang_1.1.1
## [76] later_1.3.1 munsell_0.5.0 tools_4.2.3
## [79] cachem_1.0.8 cli_3.6.1 gsubfn_0.7
## [82] generics_0.1.3 RSQLite_2.3.1 evaluate_0.21
## [85] fastmap_1.1.1 heatmaply_1.4.2 mzID_1.36.0
## [88] yaml_2.3.7 knitr_1.43 bit64_4.0.5
## [91] caTools_1.18.2 dendextend_1.17.1 KEGGREST_1.38.0
## [94] ncdf4_1.21 mime_0.12 compiler_4.2.3
## [97] rstudioapi_0.15.0 plotly_4.10.2 png_0.1-8
## [100] affyio_1.68.0 stringi_1.7.12 bslib_0.5.0
## [103] MSnbase_2.24.2 lattice_0.21-8 ProtGenerics_1.30.0
## [106] Matrix_1.6-0 tmvtnorm_1.5 vctrs_0.6.3
## [109] pillar_1.9.0 norm_1.0-11.1 lifecycle_1.0.3
## [112] BiocManager_1.30.21.1 jquerylib_0.1.4 MALDIquant_1.22.1
## [115] GlobalOptions_0.1.2 data.table_1.14.8 cowplot_1.1.1
## [118] bitops_1.0-7 seriation_1.5.1 httpuv_1.6.11
## [121] R6_2.5.1 pcaMethods_1.90.0 affy_1.76.0
## [124] TSP_1.2-4 promises_1.2.0.1 gridExtra_2.3
## [127] KernSmooth_2.23-22 codetools_0.2-19 MASS_7.3-60
## [130] gtools_3.9.4 assertthat_0.2.1 chron_2.3-61
## [133] proto_1.0.0 rjson_0.2.21 withr_2.5.0
## [136] GenomeInfoDbData_1.2.9 parallel_4.2.3 hms_1.1.3
## [139] grid_4.2.3 rmarkdown_2.23 shiny_1.7.4.1knitr::knit_exit()